Our long term goal is to understand how natural genetic variation generates morphological variation. We pursue this goal by combining approaches from developmental genetics and evolutionary biology. Recent work from our lab and others has demonstrated that alterations in gene regulation are likely to be the predominant mode of molecular change underlying morphological evolution. However, we currently have a limited understanding of the structure and function of the genomic regions that regulate gene expression. In addition, several studies have demonstrated that regulatory regions can evolve dramatically different DNA sequences while retaining conserved function. In contrast to studies of genes with conserved patterns of gene expression, almost nothing is known at the molecular level about the alterations in gene function that lead to morphological evolution. Our work is focused on identifying and characterising the DNA changes that are responsible for morphological evolution between closely related species. We have already identified some of the genes that have evolved between closely related Drosophila species to alter the patterning of fine hairs (trichomes) on the larvae and adult. We will perform a detailed investigation of the evolution of the regulatory regions of these genes by combining functional studies and phylogenetic comparisons of DNA sequence variation. Although gene regulatory regions encode much of the logic of development, it is not yet possible to read this logic directly from genomic data. An evolutionary approach to understanding the function of these gene regions is likely to provide important insights into the logic of gene regulatory regions and assist in the interpretation of comparative genomics data.